Genetics of Plant Virus Resistance

26 Jul 2005 11:58 AR AR250-PY43-23.tex XMLPublishSM(2004/02/24) P1: KUV10.1146/annurev.phyto.43.011205.141140

Annu. Rev. Phytopathol. 2005. 43:581621doi: 10.1146/annurev.phyto.43.011205.141140

Copyright c 2005 by Annual Reviews. All rights reservedFirst published online as a Review in Advance on May 2, 2005

GENETICS OF PLANT VIRUS RESISTANCE

Byoung-Cheorl Kang, Inhwa Yeam, and Molly M. JahnDepartment of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853;email: [email protected], [email protected], [email protected]

Key Words disease resistance genes, replication, cell-to-cell movement,long-distance movement, coevolution, durable resistance, plant breeding, geneticresources

Abstract Genetic resistance to plant viruses has been used for at least 80 yearsto control agricultural losses to viral diseases. To date, hundreds of naturally occurringgenes for resistance to plant viruses have been reported from studies of both monocotand dicot crops, their wild relatives, and the plant model, Arabidopsis. The isolationand characterization of a few of these genes in the past decade have resulted in detailedknowledge of some of the molecules that are critical in determining the outcome ofplant viral infection. In this chapter, we have catalogued genes for resistance to plantviruses and have summarized current knowledge regarding their identity and inheri-tance. Insofar as information is available, the genetic context, genomic organization,mechanisms of resistance and agricultural deployment of plant virus resistance genesare also discussed.

INTRODUCTION

Viruses are among the most agriculturally important and biologically intriguinggroups of plant pathogens. Plant viral diseases cause serious economic losses inmany major crops by reducing yield and quality and often determine whetherand when a crop is planted in a cropping system. Although viruses are relativelysimple genetic entities, still largely unknown are the mechanisms by which themany symptoms of disease are generated, and by which plants resist these effects.In this chapter, we review the literature pertaining to genetic resistance to plantviruses.

Genetic resistance is one of a number of approaches to protect crops fromvirus infection that also include control of biotic vectors, use of virus-free seed orplant materials, and cultural practices that minimize transmission (106). Resistantvarieties, where available, however, are still considered the most cost-effectiveand reliable approach. Considerable time and cost may be involved in developingvarieties with the appropriate range of resistances. If resistance proves durable,then the use of resistant crop varieties is clearly the preferred method to controlagricultural losses.

0066-4286/05/0908-0581$20.00 581

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.

26 Jul 2005 11:58 AR AR250-PY43-23.tex XMLPublishSM(2004/02/24) P1: KUV

582 KANG YEAM JAHN

The study of plant resistance genes (R genes), namely, plant genes in whichgenetic variability occurs that alters the plants suitability as a host, also raisesmany fundamental questions regarding the molecular, biochemical, cellular, andphysiological mechanisms involved in the plant-virus interaction and the evolutionof these interactions in natural and agricultural ecosystems. Over the past decade,the cloning and analysis of numerous plant R genes (84, 134) have stimulatedattempts to develop unifying theories about mechanisms of resistance and suscep-tibility, and coevolution of plant pathogens and their hosts. The focus has beenmainly on monogenic dominant resistance to fungal and bacterial pathogens (84);however, there is clear evidence that common mechanisms can be involved in virusresistance.

Considerable progress is evident in the areas of R gene structure, identificationof molecular interactions important in plant viral infection, and elucidation ofmechanisms of resistance and viral evolution since the last Annual Review of plantvirus resistance genes was published in 1990 (64). For this review, we emphasizethe current status of R genes that have been characterized at a molecular level,possible connections to down-stream host responses, and factors that may influencedurability of resistance in agricultural ecosystems.

TYPES OF RESISTANCE

Resistance to disease of plants has historically been divided into two major cat-egories (64): nonhost resistance and host resistance. The former, which encom-passes the case where all genotypes within a plant species show resistance or failto be infected by a particular virus, specifically signifies the state where geneticpolymorphism for susceptibility to a particular virus has not been identified in ahost taxon. Clearly, most plant species are resistant to most plant viruses. Sus-ceptibility is the exception to the more general condition of resistance or failureto infect. Although underlying mechanisms of nonhost resistance to viruses arelargely unknown and are likely as diverse for viruses as they are for other classesof plant pathogens (152), improved understanding of the ways in which infectionfails in these interactions may be particularly important for breakthroughs in thedevelopment of plants with durable broad-spectrum disease resistance.

Host resistance to plant viruses has been more thoroughly investigated, at leastin part because, unlike nonhost resistance, it is genetically accessible. This generalcase, termed host resistance, specific resistance, genotypic resistance, or cultivarresistance, occurs when genetic polymorphism for susceptibility is observed inthe plant taxon, i.e., some genotypes show heritable resistance to a particularvirus whereas other genotypes in the same gene pool are susceptible. In resistantindividuals, the virus may or may not multiply to some extent, but spread of thepathogen through the plant is demonstrably restricted relative to susceptible hosts,and disease symptoms generally are highly localized or are not evident.

The distinction between resistance to the pathogen and resistance to the diseaseis important to articulate. Resistance to the pathogen typically leads to resistance

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


VIRUS RESISTANCE GENES 583

to the disease; however, resistant responses involving necrosis can sometimes bevery dramatic, even lethal, e.g., the N gene in tobacco for resistance to Tobaccomosaic virus (TMV) (47) or the I gene in Phaseolus vulgaris for resistance toBean common mosaic virus (37). In the case of resistance to disease symptomsor tolerance to the disease, the virus may move through the host in a mannerthat is indistinguishable from that in susceptible hosts, but disease symptoms arenot observed. If the response is heritable, these plants are said to be tolerant tothe disease, although they may be fully susceptible to the pathogen. This hostresponse is very prevalent in nature, and has been used to considerable benefitin some crops, e.g., the control of Cucumber mosaic virus (CMV) in cucumber,even though the genetic control of this response is typically difficult to study (64,182). The genetics of tolerant responses are not be considered further due to thecomplexity of the biology and relative lack of information.

More recently, a third important category of host resistance has been identi-fied, initially in studies involving TMV: systemic acquired resistance (SAR). Thisresponse can be activated in many plant species by diverse pathogens that causenecrotic cell death (184), resulting in diminished susceptibility to later pathogenattack. As SAR has recently been reviewed (56), this topic is not discussed furtherhere. Virus-induced gene silencing, another induced defense mechanism to virusdisease, has also been reviewed recently (10).

Transgenic approaches to plant virus resistance have been widely explored sincethe earliest experiments where by transgenic tobacco plants expressing TMV coatprotein (CP) were challenged with TMV and shown to be resistant (74, 182, 185).It is now possible to engineer resistance and tolerance to plant viruses using trans-genes derived from a wide range of organisms including plant-derived natural Rgenes, pathogen-derived transgenes, and even nonplant and nonpathogen-derivedtransgenes. The issues related to the creation and deployment of genetically en-gineered resistance in crop breeding have been recently reviewed elsewhere (55,153, 206).

GENETICS OF VIRUS RESISTANCE IN NATURE

The first step in the study of genetics of viral resistance is to determine whether theresistant response is inherited, and if so, the number of genes involved and theirmode of inheritance. [For reviews on sources of host resistance to plant virusesand inheritance of resistance to plant viruses and viral disease, see (46, 63, 64,106, 175); for underlying general trends or common mechanisms of virus resis-tance, see (64, 65, 74, 170), and for specific crop or viral groups, see (159, 175,198).] An updated comprehensive list of published virus R genes including pre-viously summarized information based on literature through December, 2004 ispresented in Supplementary Tables 1 and 2 (Follow the Supplemental Materiallink from the Annual Reviews home page at http://www.annualreviews.org). Over200 virus R genes reported in studies of crops, their wild relatives, and the modelspecies Arabidopsis thaliana, as well as both inheritance and information about

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


584 KANG YEAM JAHN

possible mechanisms, where known, are included. Genes reported to show domi-nant inheritance are listed in Supplementary Table 1 (Follow the Supplemental Ma-terial link from the Annual Reviews home page at http://www.annualreviews.org);genes reported to show recessive inheritance are listed in Supplementary Table 2(Follow the Supplemental Material link from the Annual Reviews home page athttp://www.annualreviews.org).

This discussion highlights key observations drawn primarily from studies ofdicot species, the focus of most work to date. [For reviews on general trendsregarding inheritance of naturally occurring plant virus R genes, see (64, 65, 106,175).] Within the dicots, information regarding several plant families, notablythe Solanaceae, Cucurbitaceae, and Leguminosae, predominate for historical andagricultural reasons. R genes reported from monocot species are almost exclusivelylimited to major crop species, e.g., barley, wheat, and rice.

More than 80% of reported viral resistance is monogenically controlled; theremainder shows oligogenic or polygenic control. Only slightly more than half ofall reported monogenic resistance traits show dominant inheritance. In most butnot all (63) cases, dominance has been reported as complete. The heterozygotemay show a clearly different response from that of the homozygote, however thisis rarely checked carefully in inheritance studies. Where incomplete dominanceis observed, there are important implications for mechanisms that may involvegene dosage effects. The relatively high proportion of recessive viral R genes is inmarked contrast to fungal or bacterial resistance where most reported resistance isdominant.

About one third of the R genes listed in Supplentary Tables 1 and 2 (Fol-low the Supplemental Material link from the Annual Reviews home page athttp://www.annualreviews.org) have been tagged with molecular genetic markersincluding RFLP, AFLP, RAPD, and various other PCR-based markers. Molecularmarkers linked to R genes can be used for indirect selection via genotype, for locat-ing R genes in plant genomes, and for gene isolation. Relatively few quantitativetrait loci (QTL) for plant viral resistance have been tagged or genetically mapped(3, 12, 26, 30, 127).

Both pathogen and host taxa are composed of dynamic populations and thereforeunambiguous identification of host and pathogen genotypes is essential, ideallywith representative genotypes archived in a stable and reliable location such as theUSDA National Plant Germplasm System or the American Type Culture Collec-tion. Historically, important collections of plant germplasm and viral cultures havebeen maintained at universities and research institutes, where shifts in staffing andresource allocation may put critical genetic resources at risk.

Within a host gene pool, there may be several to many independent sourcesof resistance to a single virus or viral pathotype (a set of viral genotypes thatinteract similarly with a set of host lines showing differential response) (81, 115,159, 166). The advent of molecular methods has demonstrated that these R genesmay represent different loci with shared or independent evolutionary histories, ordifferent alleles at the same locus. Numerous early studies concluded that R genes

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.



with different resistance specificities necessarily occurred at distinct genetic loci;however, this is clearly not the case (81, 102, 169, 186). Whenever there is overlapof the resistance spectrum for a pair of alleles, genetic complementation mustbe formally assessed before different locus designations are accepted. Efforts areunder way in many plant species and, to some extent, across the plant community torationalize genetic nomenclature. Modern systems aim to reflect homology acrosssexually incompatible genera and the identity of the gene, where known.

When multiple loci control the same virus or viral pathotype, the mode ofinheritance of the resistance may be similar, as expected if the loci had arisen viaduplicative processes that have generated the high degree of redundancy observedin plant genomes (e.g., 175), or the mode of inheritance may be different (115).One way whereby independent genes for resistance to the same pathogen can bedistinguished may be the range of protection afforded by each allele.

There are a number of examples of dominant and recessive genes that appear tocontrol a relatively wide range of viral genotypes that span multiple viral species,according to current delineation of viral taxa. The most dramatic examples appearto involve members of the Potyviridae, e.g., the I gene in Phaseolus vulgaris (4)now appears to control a dominant resistance or a dominant necrotic response toten different related potyviruses, Azuki mosaic virus, Bean common mosaic virus(BCMV), Bean necrotic mosaic virus, Blackeye cowpea mosaic virus, Cowpeaaphid-borne mosaic virus, Passionfruit woodiness virus-K, Soybean mosaic virus(SMV), Thailand Passiflora virus, Watermelon mosaic virus (WMV), and Zuc-chini yellow mosaic virus (61). Furthermore, this locus has been implicated inmodulating a necrotic response to Bean severe mosaic virus, a member of the Co-moviridae (144, 145). Recombination between any of the specificities listed abovehas never been observed despite more than 75 years of backcross breeding withthis R gene, which has not been isolated, and independent sources of the I resis-tance allele show identical resistance spectra. Detailed physical mapping of the Ilocus has established that it occurs in a large cluster of TIR-NBS-LRR sequences(E. Vallejos & S. Mackenzie, personal communication).

Conversely, there are cases where resistance alleles at two or more loci arerequired to observe the resistant response. Because of the paramount agriculturalimportance of losses to BCMV, a well-known example is the bc-u system in Phase-olus vulgaris for resistance to a wide array of BCMV pathotypes. Resistance isobserved only when the bc-u locus is homozygous recessive and one or morepathotype-specific genes, bc-1, bc-2, and bc-3, are also homozygous at one ormore of three additional loci (53). In some cases, alleles at these loci affect patho-type specificity. In Capsicum, for example, full resistance is observed to anotherpotyvirus, Pepper veinal mottle virus, only when the resistance alleles pvr12 (for-merly pvr22) and pvr6 are homozygous (25). Here the pvr1 locus encodes an eIF4Ehomolog (102), and pvr6 is likely to encode eIF(iso)4E (102).

Physical clustering of distinct R genes that control different pathotypes of thesame viral species, closely related viral species, or diverse plant pathogen groups(e.g., viral, fungal, bacterial, or nematode pathogens) has also been widely noted

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


586 KANG YEAM JAHN

and discussed in terms of R gene evolution and plant breeding (142). Two distincttypes of gene clusters are clearly evident. One type of R gene cluster contains aset of genes, showing similar inheritance and resistance phenotypes that controlvery closely related viral genotypes. Presumably this type of cluster arose fromthe classic evolutionary trend of gene duplication, followed by divergence. Thismechanism classically results in genes with related but slightly altered function. Anotable example of this pattern occurs in Pisum sativum where recessive resistancehas been mapped to two R gene clusters on linkage groups II and VI. In LG II, sixvery tightly linked monogenically inherited recessive loci (bcm, cyv1, mo, pmv,sbm2, and wmv) for resistance to BCMV, Bean yellow mosaic virus (BYMV),Clover yellow vein virus (ClYVV), Pea mosaic virus (PMV), Pea seed-bornemosaic virus (PSbMV-L1), and WMV, respectively, occur in a cluster but areseparable by recombination. On LG VI, five distinct but very tightly linked locihave been identified that overlap with the specificities observed for the cluster onLG II. In this cluster, the loci cyv2, sbm1, sbm3, sbm4, and wlv confer resistanceto ClYVV, PSbMV-P1, PSbMV-L1 or -P2, PSbMV-P4, and White lupin mosaicvirus, respectively (172175).

The second type of R gene cluster contains viral resistance along with R genesthat control unrelated pathogens. These clusters may include a relatively largenumber of R genes and span megabases of genomic sequence (76). This type of Rgene cluster occurs widely in monocots and dicots. For example, the wheat Bdv1allele conferring resistance to Barley yellow dwarf virus (BYDV) is linked to fungalR genes Lr34 and Yr18 (197). This type of cluster may, in fact, emerge as the mostcommon genomic context for plant disease R genes, as more complete informationabout plant genome structure develops. Information regarding the content anddistribution of R gene clusters is probably best understood in the dicot family,Solanaceae, the focus of major investments in genetic and genomic analyses. Astomato, potato, pepper, tobacco, and many minor solanaceous crops are affectedby well-known viruses, extensive information is available regarding inheritanceand mapping of viral R genes and many other R genes (70, 76). A comprehensivegenome-wide analysis of R gene clusters and their distribution within a series ofcrop genomes linked by comparative genetic mapping has been published for theSolanaceae (76). This study clearly demonstrated that R gene clusters often occurat homologous positions in related genomic regions, even in genera that divergedtens of millions of years ago. Furthermore, across genera, clusters contained eitherdominant R genes and QTL, or recessive genes and QTL, but not both dominantand recessive genes. These clusters may therefore consist of evolutionarily relatedsequences that diverged to control very different pathogen groups. When the setsof pathogens controlled by R genes in a given cluster were compared across taxa,no overlap of resistance specificities (i.e., the group of pathogen taxa controlled byR genes in the cluster) was initially observed, except in two cases on chromosomes4 and 11. Both of these involved Phytophthora pathogens, P. capsici in pepper andP. infestans in potato. As additional R genes have been mapped, a striking patternthat includes viral R genes has now emerged (Table 1). On potato chromosome

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.



TABL

E1

Som

ecr

oss

-gen

eric

Rge

negr

oups

that

incl

ude

viru

sres

istan

cege

nesi

nSo

lana

ceae

Chr

om

oso

me

an

dre

sista

nce

gene

s

Plan

tC

hr4

Chr

5C

hr7

Chr

10C

hr11

Chr

12R

efer

ence

s

Tom

ato

Her

o(n)

Ph

-1(p)

Ph-2

(p)Ty

-2(v)

,I2(f)

,Sm

(f)

(11,6

6,85

,19

6)Po

tato

R2(p)

,Ny

(v)G

rp1

(n),G

pa(n)

,G

pa5

(n),R

1(p)

,phy

t3(p)

,Pi

1(p),R

x2(v)

,Nb

(v)

Gro

1(n)

,Rp

i1,

R9(p)

Gro

1.2

(n)R3

(p),R

6(p)

,R7

(p),

Gro

1.3

(n),p

hyt7

(p)G

pa2

(n),

Rx1

(v)(8,

39,5

8,59

,91

,112

,11

3,13

7,18

1,20

8)Pe

pper

Phyt

o5.2

(p)

L(v)

,cm

v11.

1(v)

,ph

yt3

(p)

(12,2

5,12

0)

Posit

ions

are

infe

rred,

ther

efor

eth

epr

ecise

linka

gere

latio

nshi

psoft

hese

loci

rem

ain

uncl

eari

nm

any

case

s.

Gen

enam

esar

efo

llow

edby

lette

rsde

signa

ting

the

majo

rpat

hoge

ngr

oup

contr

olle

d:(b)

bact

eria

,(f)f

ungi

,(n)n

emat

ode,

(p)Ph

ytop

htho

rasp

p.,(v

)viru

s.

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


588 KANG YEAM JAHN

12, the Rx1 gene conferring resistance to Potato virus X (PVX) is tightly linked tothe Gpa2 locus for resistance to the cyst nematode Globodera pallida (208). Thispair of specificities is also found very tightly linked in a second R gene clusteron potato chromosome 5. This cluster on chromosome 5 also contains resistanceto P. infestans. When the inferred positions of all mapped R genes from tomato,potato, and pepper are collected on one comparative genetic map, at least five Rgene groups can be discerned that contain a dominant R gene to Globodera anda dominant gene for resistance to Phytophthora, several of which also containR genes or QTL for plant viruses including PVX, as mentioned above, TMV,CMV, Tomato yellow leaf curl virus (TYLCV), and potato virus Y. A prediction,based on this observation, but not yet confirmed, is that despite these strikingdifferences in pathogen specificity, the basic molecular structure of these geneswill be generally similar, even between relatively distantly related host genera.This similarity may facilitate the molecular cloning and characterization of genesthat reside in these clusters. Insofar as this prediction has been examined withina single R gene cluster in one plant taxon, e.g., Rx and Gpa2, it has been upheld(208).

Dominant resistance is often, although not always, associated with the hyper-sensitive response (HR) (63), possibly due to the frequent use of HR as a diagnosticindicator for field resistance by plant breeders. HR, induced by specific recognitionof the virus, localizes virus spread by rapid programmed cell death surrounding theinfection site, which results in visible necrotic local lesions. HR-mediated resis-tance is a common resistance mechanism for viruses and for other plant pathogens.Because the extent of visible HR may be affected by gene dosage (37), geneticbackground, environmental conditions such as temperature, and viral genotype,etc., schemes that classify or name virus R genes based on presence or absence ofHR may obscure genetic relationships (see discussion of the Ry-mediated resis-tance to PVY in potato below).

Over the past 10 years significant advances have been made in the understand-ing of the molecular basis of the HR-mediated resistance. More than 40 plantR genes showing monogenic dominant inheritance have been cloned. Several ofthese confer resistance to plant viruses (134). These include N for resistance toTMV in tobacco (211), Rx1 and Rx2 for resistance to PVX in potato (14, 16), Sw5for resistance to Tomato spotted wilt virus (TSWV) in tomato (21), and RTM1,RTM2 to TMV (34, 212), and HRT for resistance to Turnip crinkle virus (TCV)(38), RCY1 for resistance to CMV (204), respectively, in Arabidopsis (see below).

In contrast to dominant R genes, many recessive R genes appear to functionat the single cell level or affect cell-to-cell movement. More than half of therecessive R genes identified to date confer resistance to potyviruses, members ofthe largest and perhaps the most economically destructive family of plant viruses(195). This may be a consequence of some bias that affects the scope of ourknowlege, or may be due to specific features of potyvirus biology. In general,considerably less is known regarding the mechanisms that account for recessivelyinherited resistance mechanisms. Several recessive R genes have recently been

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.



cloned and/or characterized including pvr1 (=pvr2), mo11, sbm1, and rym4/5 (67,102, 154, 186, 215), as described below.

Despite the possibility of bias affecting the comprehensiveness of availabledata, trends can be noted in the types of genetic resistance available to controlviruses belonging to specific plant virus families. For example, resistance to CMVoften shows complex inheritance. Very few monogenically inherited R genes areknown (22), despite the enormous host range of this virus and its economic impact.Most resistance or tolerance of economic significance to this pathogen is quantita-tively inherited. In contrast, resistance to tobamoviruses is widespread and is oftenmonogenic dominant. For some viral families of extreme agricultural importance,most notably the Geminiviridae, naturally occurring genetic resistance can be dif-ficult to locate, and is often highly strain-specific and/or quantitatively inherited(i.e., each gene has a relatively slight positive effect on host response), makingresistant varieties extremely difficult or impossible to develop without molecularmarkers and/or transgenic approaches.

NATURAL RESISTANCE MECHANISMS

To complete their life cycles, viruses undergo a multistep process that includesentry into plant cells, uncoating of nucleic acid, translation of viral proteins, repli-cation of viral nucleic acid, assembly of progeny virions, cell-to-cell movement,systemic movement, and plant-to-plant movement (27). Plant viruses typically ini-tiate infection by penetrating through the plant cell wall into a living cell throughwounds caused by mechanical abrasion or by vectors such as insects and nema-todes. Unlike animal viruses, there are no known specific mechanisms for entryof plant viruses into plant cells (194). When virus particles enter a susceptibleplant cell, the genome is released from the capsid, typically in the plant cytoplasm.Although not yet comprehensively analyzed, current work suggests this uncoat-ing process is not host-specific, e.g., TMV and Tobacco yellow mottle virus wereuncoated in both host and nonhost plants (107, 135). Once the genome becomesavailable, it can be translated from mRNAs to give early viral products such asviral replicase and other virus-specific proteins. Hereafter the virus faces variousconstraints imposed by the host and also requires the involvement of many hostproteins, typically diverted for function in the viral infection cycle.

Successful infection of a plant by a virus therefore requires a series of compatibleinteractions between the host and a limited number of viral gene products. Absenceof a necessary host factor or mutation to incompatibility has long been postulatedto account for recessively inherited disease resistance in plants, termed passiveresistance by R.S.S. Fraser (63, 64).

In contrast, dominant resistance has been shown in a number of plant pathosys-tems to result from an active recognition event that occurs between host andviral factors, resulting in the induction of host defense responses (modeled inFigure 1A) (64). Despite the availability of well-characterized genetic systems and

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


590 KANG YEAM JAHN

intensive investigation in this area, the biochemistry of this recognition event isstill not thoroughly understood. Genes that contribute to this response are likely tobe dominant or incompletely dominant, unless the resistant response occurs as aresult of derepression of a defense pathway (23). In theory, passive or active resis-tance can function at any stage of the virus life cycle, although most known viralresistance mechanisms appear to target virus replication or movement (Figure 1B).It is still technically difficult to quantify levels of viral accumulation with precisionin asynchronous infections of intact tissue (as opposed to protoplasts). Even withthe use of fluorescent reporter genes, the extent to which viral accumulation reflectsreplication and translation versus variations in virus movement cannot be easilydiscerned. Several lines of evidence suggest that the level of viral accumulationmay affect the ability of virus to move systemically. For example, the amount of the and protein produced by RNA 3 of Barley stripe mosaic virus can determinesystemic movement of the virus (168), and dose-dependence has been observedin a number of viral/host interactions, e.g., (37, 168). Caution may therefore beneeded before concluding that the molecular defect resulting in resistance specif-ically affects the viral infection cycle stage at which the defect, i.e., resistance, isobserved.

Cellular Resistance to Plant Viruses

Resistance at the single cell level may be characterized as a state where virusreplication does not occur, or occurs at essentially undetectable levels in inoculatedcells. This type of resistance has been termed extreme resistance (ER), cellularresistance, or immunity (63, 64). A classical example of this type of resistanceis observed when Vigna unguiculata Arlington is challenged with the ComovirusCowpea mosaic virus (CPMV) (171). A protease inhibitor that prevents CPMVpolyprotein processing was proposed as a candidate for the mechanism by whichreplication was prevented, but this has not been confirmed (171).

For plant viruses with both RNA- and DNA-encoded genomes, diverse hostfactors that are involved in or required for completion of the viral infection cyclehave been identified (Table 2). Most of these factors were identified through theanalysis of large experimental collections of mutagenized hosts (2, 213). For ex-ample, Arabidopsis mutants homozygous for the tom1 and tom2A lesions do notsupport TMV accumulation in single cells (92, 93, 158). Tom1 encodes a trans-membrane protein localized in the tonoplast that interacts with the helicase domainof the tobamovirus-encoded replicase protein (219). Tom2A also encodes a trans-membrane protein that interacts with Tom1 (207); both proteins define importantcomponents for tobamoviral replication complex (78). Another illustration of thisapproach from the Arabidopsis model was the identification of the allele lsp1, theresult of a mutation at this locus that encodes a homolog of the eukaryotic trans-lation factor eIF(iso)4E (121). When homozygous, this defect resulted in plantsthat did not support infection by Tobacco etch virus (TEV), a result presaging later

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.



TABL

E2

Exam

ples

ofh

ostf

acto

rsin

vo

lved

inpl

antv

irall

ifecy

cles

and

resis

tanc

em

echa

nism

s

Plan

tVi

rusa

Gen

eor

pro

tein

Gen

eex

pres

sion

con

tro

lEf

fect

son

vir

alin

fect

ion

Kno

wn

or

pred

icte

dpr

ote

infu

nctio

nR

efer

ence

s

Tran

slatio

nan

dre

plic

atio

nAr

abi

dops

isCL

CVA

tNSI

Ove

rex

pres

sion

Enha

nced

infe

ctio

nef

ficie

ncy

Ace

tylt

rans

fera

se(28

,136

)CM

Vss

i-2K

nock

ou

tPl

astid

-loca

lized

stea

royl

-ACP

desa

tura

se(19

3)

TEV

TuM

V1s

p1K

nock

-out

Def

ectiv

ein

TuM

Van

dTE

Vre

plic

atio

nTr

ansla

tion

initi

atio

nfa

ctor

,

eIF(

iso)4E

(121)

TMV

tom

1K

nock

-out

Affe

ctsT

MV

RN

Aac

cum

ula

tion

inpr

otop

lasts

Esse

ntia

lco

nst

ituen

tof

repl

icat

ion

com

plex

(92,9

3)

tom

2AK

nock

-out

Affe

ctsT

MV

RN

Aac

cum

ula

tion

inpr

otop

lasts

Form

atio

no

fRN

Are

plic

atio

nco

mpl

ex(20

7)

Nico

tiana

TGM

VN

bSCE

1Su

ppre

ssio

nSu

ppre

sses

TGM

Vre

plic

atio

nSU

MO

-con

jugat

ing

enzy

me

(29)

Cell-

to-c

ellm

ovem

ent

Ara

bido

psis

CMV

cum

1-1

Kno

ck-o

utCe

ll-to

-cel

lmovem

ento

fCM

Vbl

ocke

dTr

ansla

tion

initi

atio

nfa

ctor

,

eIF4

E(22

222

4)

TCV

cum

2-1

Kno

ck-o

utCe

ll-to

-cel

lmovem

ento

fCM

VB

lock

edTr

ansla

tion

initi

atio

nfa

ctor

,

eIF4

G(22

222

4)

Syste

mic

movem

ent

Ara

bido

psis

TMV

PME

Supp

ress

ion

Def

ectiv

ein

vira

lex

ito

uto

fvas

cula

rsys

tem

Pect

inm

ethy

leste

rase

(32,3

3)

aCL

CV,

Cabb

age

leaf

curl

gem

iniv

irus

;CM

V,Cu

cum

berm

osa

icvi

rus;

TEV,

Toba

cco

etch

viru

s;TG

MV,

Tom

ato

gold

enm

osa

icvi

rus;

TMV,

Toba

cco

mosa

icvi

rus;

TuM

V,Tu

rnip

mosa

icvi

rus.

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


592 KANG YEAM JAHN

observations from pepper, lettuce, pea, and tomato that implicate host translationfactors in resistance to potyviruses and CMV (102, 154, 163, 167, 186).

The second type of mechanism that can result in resistance at the single-celllevel involves an active resistant response to virus infection that occurs rapidlyenough to limit virus replication before cell-to-cell movement occurs. Plants withthis response may show no symptoms or extremely limited necrosis (pinpoint le-sions). Well-known examples of this response include resistance controlled byTm-1 for TMV in tomato (147, 209), the R gene against CPMV in cowpea (171),Nx and Rx for PVX and Ry for Potato virus Y (PVY) in potato (199), Sw5 intomato (21), and Rsv1 in soybean (80). This response has been studied in somedetail using the Ry gene for ER in potato as a model. Plants carrying the Ry gene donot show any visible symptoms when challenged with PVY. Virus accumulationis not detected in the inoculated leaves by either RNA hybridization or ELISA.Furthermore, protoplasts isolated from resistant genotypes do not support viralreplication. Because HR was not evident, it was postulated that these genes mightencode inhibitors of virus accumulation (64). However, there may be no mecha-nistic distinction between reactions previously categorized as ER and HR. Wheneach of the PVY-encoded proteins was expressed in leaves of PVY-resistant plants,the nuclear inclusion of a protease (NIaPro) induced HR, demonstrating that theHR mechanism may be a component of the ER response. The same trends holdtrue for Rx/PVX-CP in potato (14), Sw5 in tomato (21), and Rsv in soybean (79).For elicitation of Ry-mediated resistance, the protease domain of PVY NIaPro,specifically the integrity of the protease active site, is required (140). Mutant anal-ysis of NIaPro, however, demonstrated that NIa protease activity is not sufficientfor elicitation of resistance because elicitor-defective mutants still retained a highlevel of protease activity (141). The location of Ry in a genomic region containingmany NBS-LRR sequences is consistent with the possibility that Ry may encodea NBS-LRR-type protein typical of genes controlling HR (82).

Resistance to Virus Movement Within and Between Cells

Once viral multiplication has been established in the cytoplasm and/or nucleusof a single plant cell from a susceptible host, plant viruses must move from theinitially infected cells to adjoining cells, eventually resulting in systemic infection.An important class of host response to viral infection is apparent when the virusappears to establish infection in one or a few cells, but cannot move beyond theinitial focus of infection. Resistance at this level can result from either failure ofinteractions between plant and viral factors necessary for cell-to-cell movement,or from active host defense responses that rapidly limit virus spread.

As described above for viral replication and translation, intra- and intercellularviral movement also requires both virus-encoded components and specific hostfactors (27, 118). For some viral families, mainly viruses with DNA genomes,crossing the nuclear membrane represents a potential barrier for virus movement(214). For these viruses, it is necessary to import the viral genome to the nucleus

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.



for replication and export progeny genomes back to the cytoplasm for translationand virion assembly. The viral proteins required for these functions are known,at least for some viruses. For example, the nuclear import and export of bipartitegeminivirus DNA is mediated by the BV1 (BR1) protein (27), but interferencewith these processes by host factors resulting in resistance has not yet been re-ported. With respect to intercellular movement, it is well established that movementproteins (MP), identified for most families of both DNA and RNA plant viruses[for reviews, see (42, 73, 132, 188)], perform dedicated functions required forcell-to-cell movement by modifying pre-existing pathways in the plant for macro-molecular movement such that viral material can translocate between plant cells(27, 117). In the case of potyviruses, which do not encode a dedicated MP, themovement functions have been allocated to several proteins, including CP, HC-Pro, the cylindrical inclusion (CI) protein, and the genome-linked protein (VPg)(180). In mutant viruses defective in these proteins, movement from the initiallyinfected cell to adjacent noninfected cells did not occur.

A number of mutations in host genes are known that prevent cell-to-cell move-ment of plant viruses. The Arabidopsis cum1 and cum2 mutations inhibit CMVmovement (223, 224). In protoplasts prepared from plants homozygous for thesealleles, CMV RNA and CP accumulate to wild-type levels, but the accumulation ofthe CMV 3a protein, necessary for cell-to-cell movement of the virus, is stronglyreduced. Positional cloning demonstrated that CUM1 and CUM2 encode eukary-otic translation initiation factors 4E and 4G, respectively (222). Similar resultsfor members of a different viral family have been obtained from tobacco, pep-per, and pea. In tobacco, the movement of Tobacco vein mottling virus and PVYis controlled by the recessive gene va (71). In pepper and pea, pvr11 (formerlypvr21) and sbm1 were identified as mutations at a locus encoding eIF4E (67, 186).A functional analysis of the product of the dominant allele suggested a functionfor eIF4E in cell-to-cell movement, in addition to its proposed role in viral RNAreplication or translation (102, 121).

The HR also serves to disrupt cell-to-cell movement of plant viruses. Recog-nition of the viral elicitor results in the induction of a cascade of host defenseresponses that include oxidative H2O2 bursts and up-regulation of hydrolytic en-zymes, PR proteins, and callose and lignin biosynthesis. As a consequence, viralmovement may be limited to a small number of cells, illustrated by such classicexamples as the tobacco N gene (160) and the tomato Tm-2 and Tm-22 alleles(147). Protoplasts isolated from the plants carrying these R genes allowed repli-cation of TMV; no cell death was observed. Despite the strong correlation of HRand disease resistance, necrotic cell death is now thought to be an ancillary con-sequence of the resistant response, not necessary for pathogen suppression. Forexample, in Phaseolus vulgaris carrying the I allele to BCMV, a continuum of viralinfection phenotype responses that range from no necrosis to a lethal systemic re-sponse can be manipulated by allele dosage and temperature (37). The defense nodeath (dnd1) mutant in Arabidopsis is another example of independent resistanceand HR (225), consistent with results from several viral-host systems including

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


594 KANG YEAM JAHN

Sw-5-mediated resistance against Tomato spotted wilt virus (21), Rsv-1-mediatedvirus resistance to SMV in soybean (80), and resistance against Cauliflower mo-saic virus in tobacco (36). Furthermore, when HRT was introgressed into Col-1,most of the HRT-transformed plants developed HR upon TCV infection, yet thevirus spread systemically without systemic necrosis (38).

Resistance to Long-Distance Movement

In susceptible hosts, plant viruses that do not show tissue restrictions move fromthe mesophyll via bundle sheath cells, phloem parenchyma, and companion cellsinto phloem sieve elements (SE) where they are translocated, then unloaded ata remote site from which further infection will occur (27, 188). This pathway istypically part of an elaborate symplastic network in plants through which virusesestablish systemic infection (130). Plasmodesmata, elaborate and highly regulatedstructures with which viruses interact for both cell-to-cell and long-distance move-ment, provide symplastic connectivity between the epidermal/mesophyll cells andcells within the vasculature, including sieve elements (27, 131, 188). Entry intothe SE-companion cell complex is currently thought to be the most significantbarrier to long-distance movement (50, 216). Once present in a companion cell, avirus potentially has direct access to the sieve tube, the conducting element of thephloem that serves as the pathway for both nutrient and virus transport throughoutthe plant (117).

Virus particles loaded in the phloem apparently follow the same pathway asphotoassimilates and other solutes, albeit not necessarily via strictly passive pro-cesses (149, 188). Most plant viruses require CP for long-distance movement,independent of any requirement for CP in cell-to-cell movement. Analysis of CPmutants for a number of viruses including TMV and TEV suggests that CP is es-sential for entry into and/or spread through sieve elements (117, 118). Some DNAviruses also require CP for long-distance movement (20), although other whiteflytransmitted geminiviruses do not require CP for systemic infection (68). Phl-oem-limited viruses, e.g., Luteovirus, are typically limited to phloem parenchyma,companion cells, and SE, and apparently lack the ability to exit phloem tissue (205)or possibly to infect nonphloem tissue (9). A few viruses, most notably members ofthe Sobemovirus genus, use xylem for long-distance movement. The mechanismsof viral interaction with xylem are largely unknown (117, 146).

Because systemic movement is more difficult to study than cell-to-cell move-ment, relatively few host factors that are essential for this process thereby definingpotential R gene candidates have been identified to date. Down-regulation of pectinmethylesterase, shown to interact with TMV MP, resulted in impaired movementof TMV, probably by blocking virion exit from phloem. This finding is consistentwith the hypothesis that phloem loading and unloading of virus involve distinctfactors (32).

Some examples of natural virus resistance appear to involve mechanisms thatnegatively affect systemic movement. For instance, the V20 strain of tobacco

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.



exhibits a strain-specific defect in supporting systemic infection by TEV (190).Using a TEV clone that expressed a reporter protein, -glucuronidase (GUS),genome amplification, cell-to-cell and long-distance movement were measured inV20 tobacco and a susceptible line. Long-distance movement from leaf to leaf wasmarkedly restricted in V20, associated with reduced entry into and exit from SE.This trait was attributed to the interaction of two unlinked, unidentified recessivegenes. These data support the hypothesis that long-distance movement requiresa set of host functions distinct from those involved in cell-to-cell movement. Inanother case, Cowpea chlorotic mottle virus (Bromoviridae) infects and movescell-to-cell through inoculated leaves of soybeans homozygous for two recessivegenes but entry into vascular tissue is restricted (75). In potato, the recessive raallele, when homozygous, completely blocks vascular transport of Potato virus A(PVA) in graft-inoculated plants (82). Given the degree of conservation observedfor some basic functions in plants, fundamental knowledge about the structureand function of plant vasculature will likely be relevant as efforts to identify thesegenes proceed.

In some cases, systemic movement is not prevented but delayed and reduced.In Capsicum genotypes homozygous for the resistance allele pvr3, Pepper mottlevirus (PepMoV-FL) accumulated in inoculated leaves and moved into the stem butdid not enter internal phloem for systemic movement to young tissues (77, 151,228). Infection by a second virus, CMV, alleviated this restriction, which suggeststhat CMV was able to compensate for the defect in the host, either by providinga factor that facilitates movement of both viruses or alleviating the restriction byan unknown mechanism (151, 228). A similar type of resistance was describedfor CMV whereby virus remained localized to the lower portions of the plant (54,156). Dufour et al. (54) showed that CMV accumulated in external but not internalphloem in the petiole of the inoculated leaf and the lower stem of the resistantgenotype. Derrick & Barker (44) evaluated potato lines resistant to Potato leafrollvirus (PLRV) and showed that the resistance was associated with an exclusion ofvirus from external phloem bundles, whereas virus occurred in both internal andexternal phloem in the susceptible line. Again, the identity of these genes in thehost and their role in viral infection are unknown.

Relatively few dominant genes are known for resistance to systemic movementof plant viruses. The Arabidopsis RTM system is one exception. Many A. thalianaecotypes support TEV replication and cell-to-cell movement in inoculated leavesbut do not allow systemic movement. The loci RTM1, RTM2, and RTM3 are re-quired for restriction of long-distance movement of TEV (132, 212). Resistancemediated by the RTM genes is specific to TEV and does not involve a hypersensi-tive response or induction of SAR. RTM1 and RTM2 were isolated by map-basedcloning. The deduced RTM1 protein is similar to the Artocarpus integrifolia lectin,jacalin. Jacalin belongs to a family of proteins with members that are implicatedin defense against insects and fungi. The deduced RTM2 protein contains sev-eral domains including an N-terminal region with similarity to plant small heatshock proteins (34). Both these genes are expressed in phloem, specifically SEs,

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


596 KANG YEAM JAHN

but the mechanism by which TEV movement in this system is restricted is notunderstood.

DOMINANT PLANT VIRUS RESISTANCE GENESCHARACTERIZED AT THE MOLECULAR LEVEL

Most plant disease-resistance (R) genes isolated and characterized to date representgenes whose recognition of their cognate pathogens has been modeled as gene-for-gene interactions (62, 103). Under this well-known model, complementarypairs of dominant genes are defined by the host-pathogen interaction, one in thehost and the other in the pathogen, whose physical interaction, direct or throughintermediates, determines the outcome of the encounter (134). Following pathogenrecognition, which occurs via poorly defined mechanisms, the R gene is presumedto activate a signaling cascade that coordinates plant defense responses to blockpathogen spread, resulting in an incompatible interaction. Nine dominant plantvirus R genes have been isolated and sequenced to date: HRT, RTM1, RTM2,RCY1 from Arabidopsis; and from solanaceous hosts, N, Rx1, Rx2, Sw5, and Tm-22 (Table 3). Except for RTM1 and RTM2 discussed above, all of these clonedvirus R genes share structural similarity. HRT, Rx1, Rx2, RCY1, Sw5, and Tm-22 are Class 2 R genes, proteins that contain a region of leucine-rich repeats(LRRs), a putative nucleotide binding domain (NBS), and an N-terminal putativeleucine-zipper (LZ), or other coiled-coil (CC) sequences (83, 134) (Figure 2A).The N gene belongs to the Class 3 R gene family, which is similar to Class 2but with a domain similar to the N terminus of the Toll and Interleukin 1 receptor(TIR) protein instead of the CC domain (6) (Figure 2A). Class 2 and Class 3 Rproteins lack a transmembrane domain consistent with the intracellular locationof viral avirulence factors. These genes define the plant viral pathosystems aboutwhich the most is known at the molecular and cellular levels.

Resistance to Tobacco Mosaic Virusin Tobacco Conferred by N

The N gene, introduced into tobacco from Nicotiana glutinosa, is a single dominantgene for HR to TMV that defines a classic model system for plant-virus interaction(89) and for the study of SAR (184). Below 28C, tobacco plants carrying the Nallele develop necrotic local lesions within 48 h at the site of TMV inoculation (89,184). At higher temperatures, however, HR does not develop, and TMV spreadssystemically throughout the plant. If a plant is initially infected at a temperaturethat allows systemic TMV infection and then subsequently moved to a lowertemperature, a lethal systemic necrotic response is observed (47).

The N gene was isolated by insertional mutagenesis using the activator (Ac)transposon system (211) and confirmed by transgenic complementation (49).Deletion- and site-directed mutagenesis indicated that the TIR, NBS, and LRRdomains are all required for proper function, although their role in HR is not

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.

10 Aug 2005 16:42 AR AR250-PY43-23.tex XMLPublishSM(2004/02/24) P1: KUV


TABL

E3

Nat

ural

lyo

ccu

rrin

gpl

antv

irusr

esist

ance

gene

sfor

whi

chn

ucl

eotid

ese

quen

cesa

rekn

own

Gen

ePl

ant

Viru

saR

esist

ance

mec

hani

smC

loni

ngm

etho

dPr

edic

ted

dom

ains

Yea

riso

late

dR

efer

ence

s

NN.

taba

cum

TMV

Cell-

to-c

ellm

ovem

ent(

HR)

Tran

spos

onta

ggin

gTI

R-N

BS-L

RR19

94(21

1)Rx

1S.

tube

rosu

mPV

XR

eplic

atio

nPo

sitio

nalc

loni

ngCC

-NBS

-LRR

1999

(14)

Rx2

S.tu

bero

sum

PVX

Rep

licat

ion

Posit

iona

lclo

ning

CC-N

BS-L

RR20

00(16

)Sw

5S.

escu

lent

umTS

WV

Cell-

to-c

ellm

ovem

ent(

HR)

Posit

iona

lclo

ning

CC-N

BS-L

RR20

00(21

)H

RTA.

thal

iana

TCV

Cell-

to-c

ellm

ovem

ent(

HR)

Posit

iona

lclo

ning

LZ-N

BS-L

RR20

00(38

)RT

M1

A.th

alia

naTE

VSy

stem

icm

ovem

ent

Posit

iona

lclo

ning

Jaca

linlik

ese

q20

00(34

)RT

M2

A.th

alia

naTE

VSy

stem

icm

ovem

ent

Posit

iona

lclo

ning

Jaca

linlik

ese

q20

00(21

2)RC

Y1A.

thal

iana

CMV

Cell-

to-c

ellm

ovem

ent(

HR)

Posit

iona

lclo

ning

CC-N

BS-L

RR20

02(20

4)Tm

22S.

lyco

pers

icum

ToM

VCe

ll-to

-cel

lmovem

ent(

HR)

Tran

spos

onta

ggin

gCC

-NBS

-LRR

2003

(116)

pvr1

,pv

r12

C.a

nn

uu

mPV

YR

eplic

atio

nCa

ndid

ate

appr

oach

eIF4

E20

02(10

2,18

6)pv

r11

Cell-

to-c

ellm

ovem

ent

mo

11m

o12

L.sa

tiva

LMV

Rep

licat

ion

Tole

ranc

eCa

ndid

ate

appr

oach

eIF4

E20

03(15

4)

sbm

1P.

sativ

umPS

bMV

Rep

licat

ion

Cand

idat

eap

proa

cheI

F4E

2004

(67)

aCM

V,Cu

cum

berm

osa

icvi

rus;

LMV,

Lettu

cem

osa

icvi

rus;

PSbM

V,Pe

ase

edbo

rne

mosa

icvi

rus;

PVY,

Pota

tovi

rusY

;PV

X,P

ota

tovi

rusX

;TCV

,Tu

rnip

crin

kle

viru

s;To

MV,

Tom

ato

mosa

icvi

rus;

TEV,

Toba

cco

etch

viru

s;TM

V,To

bacc

om

osa

icvi

rus;

TSW

V,To

mato

spot

ted

wilt

viru

s.

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


598 KANG YEAM JAHN

known (6, 125). Furthermore, N transcription is up-regulated by TMV infection(123), producing two transcripts via alternative splicing. Both translation productsare necessary at an optimum ratio for resistance to be achieved (48). Transcrip-tional activation of several WRKY and MYB transcription factors also results fromthe N-TMV interaction (21, 220, 221).

Rar1, SGT1, and EDS1, required for signal transduction mediated by mostknown R genes, are also required for the N genemediated resistance in tobacco(125, 126) (Figure 2B). It is hypothesized that SGT1 and Rar1 associate withHsp90 as cochaperones in the assembly or conformational regulation of N pro-tein complexes (124). The multiprotein complex, the COP9 signalosome, whichphysically interacts with SGT1, is also implicated in N genemediated signaling(125). In this signaling cascade, two mitogen-activated protein kinases (MAPK), awound-inducible protein kinase (WIPK), and SA-inducible protein kinase (SIPK)are activated (226) by an upstream MAPK kinase (MAPKK), NtMEK2 (178). Si-lencing WIPK, SIPK, or NtMEK2 attenuates N gene resistance (100) (Figure 2B).

Resistance to Potato Virus X in PotatoConferred by Rx1 and Rx2

The Rx loci in potato, Rx1 on chromosome V and Rx2 on chromosome XII (181),confer resistance to PVX in the absence of necrotic cell death. Rx-mediated resis-tance results in a very rapid arrest of PVX accumulation in the initially infected cell(111). In contrast to HR-associated resistance, Rx-mediated resistance is active inprotoplasts (1, 15, 111). When protoplasts isolated from resistant (Rx) and suscep-tible (rx) potato genotypes were inoculated with PVX and TMV, Rx protoplastsshowed



domains such that they are no longer held inactive (P. Moffet & G. Rairdan, per-sonal communication). In experiments designed to determine the biochemistry ofRx function, segments of the protein were expressed independently in an elegantsystem where phenotypic response could be easily assayed. PVX CP-dependentHR was observed after fragments of Rx (CC and NBS-LRR domains) and PVX-CP were expressed transiently in N. benthamiana via agroinfiltration (143). Theseresults indicate that a functional Rx protein can be reconstituted through physicalinteractions between domains, even when the domains are expressed in differentmolecules. Furthermore, PVX CP disrupted the interaction between these Rx-derived domains. The current model suggests that CP recognition induces sequen-tial conformational changes in Rx, disrupting intramolecular interactions, therebyactivating Rx-mediated signaling (143).

Experiments using virus-induced gene silencing (VIGS) showed that Rx-mediated resistance does not require EDS1 (164) and RAR1. Bieri et al., however,have shown that silencing Rar1 actually reduces the levels of Rx (18). Therefore,Rar1 is likely a cochaperone required to varying degrees by different R proteins(P. Moffet, personal communication). Silencing of tobacco MAP kinase kinasekinase (MAPKKK) interferes with the function of the Rx gene (99, 100). Simi-lar to results described above for the N gene, silencing SGT1 also compromisedRx-mediated resistance (165), and HSP90 is required, presumably acting as acochaperone to stabilize Rx (129) (Figure 2B).

Resistance to Tomato spotted wilt virusin Tomato Conferred by Sw-5

Economic considerations have promoted the goal of TSWV-resistant tomato va-rieties in plant breeding programs for nearly 70 years. Early genetic studies re-ported five genes, Sw-1a, Sw-1b, sw-2, sw-3, and sw-5, from two species, Solanumpimpinellifolium and Solanum lycopersicum (60, 90), all of which were overcomequickly. Sw-5, introgressed from Solanum peruvianum into tomato, has demon-strated broad and stable resistance (183, 200). In resistant genotypes, local necroticlesions develop on inoculated tissue, and systemic movement of the virus is re-stricted. The Sw-5 locus was isolated by positional cloning and sequenced, reveal-ing that the resistance allele encodes a CC-NBS-LRR R protein. Sw-5 is remark-ably similar to the tomato Mi gene for nematode resistance with the exception offour heptad amphipathic leucine zippers at the N terminus (21). This pronouncedsimilarity suggests that Sw-5 and Mi may share a common signal transductionpathway. Sw-5 and its paralogs were mapped to tomato chromosome 9 and chro-mosome 12 with other fungal, viral, and bacterial R genes. A comparative analysiswith the genus Capsicum, which is considerably diverged from Solanum withinthe tribe Solanae, indicated that paralog position was largely conserved betweenthese genera (94). In Capsicum, monogenic dominant TSWV resistance conferredby Tsw showed identical resistance phenotype and strain-specificity to Sw5, butno cross-hybridization with Sw5 was detected. When resistance-breaking TSWV

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


600 KANG YEAM JAHN

strains were analyzed, avirulence determinants mapped to different subgenomicRNAs (94).

Resistance to Tomato mosaic virus in TomatoConferred by Tm22

Tm22, the second tobamovirus R gene isolated, is one of the three R genes, Tm1,Tm2, and Tm22, used widely in tomato breeding to control Tomato mosaic virus(ToMV) (81, 166). The Tm1 gene from S. hirsutum confers extreme resistanceand was mapped to chromosome 2. Tm2 and Tm22, considered to be alleles fromS. peruvianum, are located close to the centromere of chromosome 7 (81). Tm22,considered the more durable of the two alleles, was isolated by transposon taggingand encodes an 861 amino acid CC-NBS-LRR protein (116). The predicted proteinfrom the susceptible allele tm2 also encodes a CC-NBS-LRR protein that appearscomparable in most respects to the protein encoded by the resistance allele. Anal-ysis of the nucleotide sequence of resistance-breaking virus isolates indicated thatthe MP protein is the avirulence factor in this resistance system (24, 210). However,different mutations are required to overcome Tm2 and Tm22.

Resistance to Turnip crinkle virus in ArabidopsisConferred by HRT

A single dominant gene, HRT, was identified for HR resistance to TCV (41). HRTis located on chromosome 5 and encodes a CC-NBS-LRR protein with strikingsimilarity to the RPP8 gene family for resistance to the oomycete Peronosporaparasitica (38). Despite very high sequence similarity, HRT and RPP8 specificallycontrol only their cognate pathogens. Analysis of resistance in HRT-expressingtransgenic plants indicated that HRT is necessary but generally insufficient forresistance. About 90% of the HRT-transformed Col-0 plants developed HR andexpressed PR-1 after TCV infection yet remained susceptible to TCV. Full resis-tance to TCV required both HRT and a recessive allele rrt (38). Later experimentsdemonstrated that the HRT-/rrt-mediated response is dependent on EDS1 and in-dependent of RAR1 and SGT1 (31). In this system, TCV CP is the avirulence de-terminant recognized by HRT (38). A host protein, TIP (TCV interacting protein)that belongs to the NAC family of transcriptional activators is known to interactwith TCV CP. Although the relevance of this interaction to the mechanism of re-sistance remains unclear, this interaction apparently functions to keep TIP out ofthe nucleus (179).

Resistance to Cucumber mosaic virus in ArabidopsisConferred by RCY1

Extensive examination of 12 Arabidopsis ecotypes identified a CMV-Y-resistantecotype, C24 (201). The resistance response of C24 includes suppression of virusmultiplication to a low level, the formation of necrotic lesions at the primary site

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.



of virus infection, and restriction of virus to the inoculated leaves. This resistanceresponse in C24 is controlled by a single dominant RCY1 (resistance to cucumbermosaic virus strain Y) gene. The analysis of a series of chimeric viruses constructedfrom the avirulent isolate CMV-Y and the virulent isolate CMV-B2 revealed thatthe coat protein of CMV-Y serves as the avirulent determinant of resistance inC24 (204). The RCY1 gene has been mapped in Arabidopsis within the MRC-5region on chromosome 5, in which nine other defined resistance genes (RAC3,RPS4, HRT, TTR1, and five distinct RPP loci) are located (204). Fine mappingand sequence comparison of this region from C24 and a CMV-Y susceptible C24mutant identified the RCY1 gene encoding 104-kDa CC-NBS-LRR type protein.RCY1 is allelic to the resistance gene RPP8 against Peronospora parasitica inthe ecotype Lansberg erecta and HRT against TCV in the ecotype Dijon-17. TheRCY1-conferred resistance requires both salicylic acid and ethylene signaling butnot jasmonic acid signaling (202, 203).

RECESSIVE PLANT VIRUS RESISTANCE GENESCHARACTERIZED AT THE MOLECULAR LEVEL

Despite notable progress towards defining the elements that comprise dominantR gene-mediated defense responses in plants, little is known about the nature ofplant susceptibility to disease. Owing to the relatively small number of proteinsthey encode, viruses completely depend on the host factors to complete their lifecycle (2, 213). Typical plant viruses encode 4 to 10 proteins that coordinate thecomplex biochemistry and intermolecular interactions required for viral infectioncycles. Studying recessive virus resistance provides a unique opportunity to revealhost factors required for susceptibility and mechanisms of pathogenesis of thepathogen. Recent findings have confirmed early theoretical predictions (describedabove) that mutations of some host factors will result in recessively inheritedresistance to plant viruses. The identification and characterization of host factorsin which mutations interrupt viral pathogenesis will provide a new opportunityfor understanding viral pathogenesis itself, as well as host responses; this is anapproach that has been unavailable to date in the study of dominant resistance.Whether as a consequence of the economic importance of the Potyviridae, therelative prevalence of recessive resistance to this group of viruses, and/or therelative ease with which these viruses can be experimentally manipulated, studiesof recessive R genes to date have focused largely on this viral family.

Several host genes whose mutations impair the infection cycle of plant viruses,including BCTV, CMV, TEV, TuMV, TMV, TGMV, and TCV, have been identifiedand characterized in Arabidopsis (Table 2). The translation initiation factor eIF4Ehas been identified repeatedly as a naturally occurring recessively inherited resis-tance locus in pepper pvr1 (102, 186), lettuce mo1 (154), and pea sbm1 (67) andhas been implicated in barley as a candidate for rym4/5 (167) (Table 3). The eIF4Eisoform eIF(iso)4E also has been implicated in Arabidopsis and pepper resistance

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


602 KANG YEAM JAHN

(102, 121). The role of eIF4E and eIF(iso)4E in the potyvirus infection cycle is notknown. However, the negative effects of mutations in these host factors on the in-fectivity of various potyviruses in various host plants imply that the effect of thesehost factors upon potyvirus infection cycle is probably conserved. The commonfeature linking pvr1/2, sbm1, and mo1 is that the viral avirulence determinants mapto a specific region in the VPg, the protein covalently linked to the 5 end of the viralRNA and perhaps mimicking the m7G cap of eukaryotic mRNAs (19, 104, 105,148). In eukaryotic cells, eIF4E binds to the m7G cap as the first step in recruitingmRNA into the translational preinitiation complex. A similar role for eIF4E mightbe predicted when potyvirus infects plant cells (102). Although eIF4E has neverbeen shown to bind VPg in infection, VPg or its precursor VPg-Pro interacted witheIF4E or eIF(iso)4E in yeast two-hybrid and in vitro pull-down assays (102, 122,190, 217).

In the 1950s, pvr1 and pvr2 in pepper (Capsicum annuum and C. chinense)were initially considered allelic but then two loci were distinguished because ofdifferences in resistance spectra. The allele formerly known as pvr21 is effectiveonly against PVY-0, and pvr22 is effective against both PVY-0 and PVY-1. Theallele pvr1 was relatively broad in effect, controlling TEV, PepMoV, and PVY)(115). We now know that only one locus is involved, pvr1, at which at least threeresistance alleles and two susceptibility alleles occur (186). Point mutations ineIF4E that fall near critical positions for cap-binding function abolish interactionwith TEV VPg and determine the range of isolates across three potyviral speciesthat are controlled (102). Two of these alleles when homozygous block accumu-lation of the virus in protoplasts (43, 150). The narrower spectrum allele retardsmovement of the virus through the plant but has no effect at the protoplast level(5). In a fourth case, Pepper veinal mottle virus, it appears eIF4E and probablyeIF(iso)4E must be mutated to control the virus (102).

In lettuce, mo11 and mo12 control common isolates of LMV. In the homozygousstate, mo11 confers resistance, i.e., absence of LMV accumulation; mo12 results inreduced LMV accumulation and lack of symptoms (180). As observed in pepper,allelic variants of eIF4E, Ls-eIF4E0, Ls-eIF4E1, and Ls-eIF4E2 contained pointmutations that result in predicted amino acid substitutions near the cap-bindingpocket of the protein (154).

In pea, sbm1 confers resistance to PSbMV pathotypes P1 and P4 as describedabove, now known to be a consequence of mutations in an eIF4E homolog (67).Transient expression of susceptible-eIF4E in a resistant background complementedPSbMV infection by supporting both virus multiplication in primary target cellsand cell-to-cell movement. Processes that account for cell-to-cell movement arenot well understood, and therefore it is difficult to speculate on a plausible rolefor eIF4E in virus movement. Nevertheless, in both the pepper and pea systems,variants at an eIF4E locus result in inhibition of movement, as well as extremeresistance. Again, point mutations in the resistant eIF4E allele are located in andaround the cap-binding pocket. Similar to pvr1, cap-binding ability of the eIF4Eprotein is abolished in the resistant eIF4E variant. Recently, rym4/5 for resistanceto BaYMV in barley has also been shown to encode eIF4E (215). In contrast

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.



to dominant R genes where resistance to the same or closely related pathogensgenerally do not occur in syntenic positions, a recessive potyvirus R gene pot1from tomato was mapped to a collinear position with pepper gene pvr2 (163).These results indicate that recessive R genes are highly conserved. Evidence todate indicates that, for the most part, dominant and recessive R genes may not berelated mechanistically and evolutionarily.

COEVOLUTION OF VIRUS RESISTANCE AND VIRALAVIRULENCE GENES

Avirulence genes in plant pathogens have been defined by their requirement fordisease resistance in hosts containing corresponding R genes (62, 103). Plantviruses evolve very rapidly owing to very short replication cycles, large numbersof genomes within each cell across many cells per host, and many hosts. For RNAviruses, the absence of a proofreading function in viral replicases may result in mu-tation rates as high as 104 per replication cycle per base (52). Viral genetic variationcan result from several major genetic processes including mutation, recombination,and the acquisition of additional genomic sequence. As a consequence, resistance-breaking viral genotypes are known for most host resistance, especially for genesshowing HR. Avirulence determinants are typically identified by creating chimericclones derived from viral genotypes with contrasting virulence and then testingfor infectivity. Once an avirulence domain is identified, site-directed mutagenesisallows identification of specific point mutations responsible for virulence. Table 4lists R genes and corresponding viral avirulence factors identified to date.

Virtually any part of the viral genome can define an avirulence determinant. Withrespect to R genes that confer HR, avirulence factors include viral RNA polymerasesubunits, movement protein, and CP. Several potyviral avirulence genes have beenidentified for dominant R genes that do not show HR. The CI and P3 proteins ofTurnip mosaic virus serve as avirulence determinants for the Brassica napus Rgenes, TuRBO1 and TuRBO4/5 (9698), while SMV HC-Pro and P3 are involvedin overcoming Rsv1 in soybean (57).

In contrast to the case for dominant genes where many different viral com-ponents have been identified as avirulence determinants, a pronounced trend isapparent viral factors that serve as the determinant for pathogenicity in resistancesystems controlled by recessively inherited R genes. Of nine R gene studies todate, seven identify potyviral VPg as the pathogenicity determinant for recessiveresistance, although the systems in question show diverse resistance phenotypes:Capsicum pvr1/pvr12 resistance to PVY is cellular (148), tobacco va resistanceimpairs the cell-to-cell movement (155), and Nicandra physaloides and Solanumcommersonii affect long-distance movement (177). The eighth study, also focusedon a potyviral system, PsbMV/pea, identified the P3-6K1 cistron as the pathogenic-ity determinant (101). Only one study to date has focused outside the Potyviridae.In this case, the 3 untranslated region of the carmovirus Melon necrotic spotvirus (MNSV) genomic RNA defined the location of the viral determinant in the

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


604 KANG YEAM JAHN

TABL

E4

Vira

lav

irule

nce

dete

rmin

ants

and

thei

rco

rres

pond

ing

plan

tres

istan

cege

nes

Plan

tR

esist

ance

gene

Viru

saAv

irul

ence

gene

Rep

orte

dm

esist

ance

mec

hani

sm

Res

istan

ce-

brea

king

chan

geR

efer

ence

s

Ara

bido

psis

HRT

TCV

Coat

prot

ein

HR

Not

avai

labl

e(15

7,21

8)RC

Y1CM

VCo

atpr

otei

nH

RN

otav

aila

ble

(204)

Bea

nBd

mB

DM

VB

V1

prot

ein

HR

Not

avai

labl

e(69

)Br

ass

ica

na

pus

TuRB

O1,

TuRB

O1b

TuM

VCI

HR

Sing

leaa

(96)

TuRB

O3

TuM

VP3

Sing

leaa

(98)

TuRB

O4,

TuRB

O5

TuM

VP3 CI

Rep

licat

ion

HR

Sing

leaa

Sing

leaa

(97)

C.a

ma

ran

ticol

orCa

MV

Gen

eV

Ipro

duct

Not

avai

labl

e(10

9,19

1)Co

wpe

aCM

V2a

poly

mer

ase

HR

Sing

leaa

(108)

Cucu

mis

mel

oL.

nsv

MN

SV3

porti

ono

fMN

SVge

nom

eR

eplic

atio

n3

UTR

(45)

Lettu

cem

o11

mo

12LM

V3

half

ofg

enom

eR

eplic

atio

nm

ovem

ent

Not

avai

labl

e(17

8)

Nica

ndra

phys

aloi

des

PVA

-M62

Kan

dV

PgSy

stem

icm

ovem

ent

Fou

raa

(177)

Pea

sbm

-1PS

bMV

VPg

Rep

licat

ion

Not

avai

labl

e(10

5)sb

m-2

PSbM

VP3

and

6K1

cistr

onN

otav

iala

ble

(101)

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.



Pepp

erL1

,L2

,L3

TMV

Coat

prot

ein

HR

Not

avai

labl

e(17

,40,

72)

pvr1

1

pvr1

2PV

YV

PgM

ovem

ent

Rep

licat

ion

Sing

leaa

(148)

Pota

toNb

PVX

25K

movem

entp

rote

inH

RSi

ngle

aa(13

3)Nx

PVX

Coat

prot

ein

HR

Sing

leaa

(189)

Rx1,

Rx2

PVX

Coat

prot

ein

Rep

licat

ion/

HR

Two

aa(15

)Ry

PVX

NIa

prot

ease

Rep

licat

ion

Not

know

n(14

0)To

bacc

oN

To

MV

Coat

prot

ein

HR

Sing

leaa

(110,

187)

Toba

cco

NTM

VR

eplic

ase

(helic

asedo

mai

n)H

RSe

ver

alaa

(162)

vaPV

YV

PgCe

ll-to

-cel

lSi

ngle

aa(15

5)N.

clev

elan

dii

TBSV

P22

movem

entp

rote

inCe

ll-to

-cel

lm

ovem

ent

Not

avai

labl

e(35

,192

)

Tom

ato

Tm-1

ToM

VR

eplic

ase

Rep

licat

ion

Two

aa(13

8)Tm

-2,

Tm-2

2To

MV

30kD

movem

entp

rote

inH

RTw

oaa

(139,

210)

pot-1

PVY

VPg

Sing

leaa

(148)

Sw-5

TSW

VM

RN

AH

RM

utip

leaa

(87)

Soyb

ean

Rsv1

SMV

HC-

Pro

and

P3ci

stron

(57)

aB

YM

V,Be

anye

llow

mosa

icvi

rus;

CaM

V,Ca

uliflo

werm

osa

icvi

rus;

CMV,

Cucu

mbe

rm

osa

icvi

rus;

LMV,

Lettu

cem

osa

icvi

rus;

MN

SV,

Mel

onnec

rotic

spot

viru

s;PS

bMV,

Pea

seed

born

em

osa

icvi

rus;

PVA

-M

,Pota

tovi

rus

Ast

rain

M;P

VY,

Pota

tovi

rus

Y;PV

X,P

ota

tovi

rus

X;T

BSV

,To

mato

bush

stun

tvi

rus;

TCV,

Turn

ipcr

inkl

evi

rus;

TuM

V,Tu

rnip

mosi

cvi

rus;

ToM

V,To

mato

mosa

icvi

rus;

TMV,

Toba

cco

mosa

icvi

rus;

TVM

V,To

bacc

ove

inm

ottl

ing

viru

s;TS

WV,

Tom

ato

spot

ted

wilt

viru

s;SM

V,So

ybea

nm

osa

icvi

rus.

Ann

u. R

ev. P

hyto

path

ol. 2

005.

43:5

81-6

21. D

ownl

oade

d fro

m w

ww

.annu

alre

view

s.org

by M

onas

h U

nive

rsity

on

10/2

1/12

. For

per

sona

l use

onl

y.


606 KANG YEAM JAHN

interaction of MNSV with melon (45). In the eight cases where the viral elici-tor is protein, host recognition of these viral proteins that serve as pathogenicitydeterminants is altered by amino acid substitutions that do not appear to signifi-cantly compromise the function of the protein in pathogenesis. For other microbialpathogens, there often appears to be a fitness penalty association with mutationsfrom avirulence to virulence (128). Although this type of fitness/avirulence trade-off has not been noted generally for plant viruses, there are specific examples wherethis occurs. Isolates of ToMV capable of overcoming Tm22 gene were found tomultiply poorly on resistant plants (116). If the Tm22 resistant protein targets adomain of the viral MP such that this pr

Date post:	16-Dec-2015
Category:	Documents
Upload:	monica-andrea-arias
View:	217 times
Download:	0 times

Genetics of Plant Virus Resistance

Documents